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2. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Author

Mock, Thomas, Otillar, Robert P, Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J, Allen, Andrew E, Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W, Falciatore, Angela, Ferrante, Maria I, Fortunato, Antonio E, Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G, Kroth, Peter G, Leese, Florian, Lindquist, Erika A, Lyon, Barbara R, Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A, Uhlig, Christiane, Valas, Ruben E, Valentin, Klaus U, Worden, Alexandra Z, Armbrust, E Virginia, Clark, Matthew D, Bowler, Chris, Green, Beverley R, Moulton, Vincent, van Oosterhout, Cock, and Grigoriev, Igor V

Subjects
Diatoms, Carbon Dioxide, Iron, Gene Expression Profiling, Genomics, Ice Cover, Acclimatization, Evolution, Molecular, Phylogeny, Recombination, Genetic, Genetic Drift, Alleles, Genome, Darkness, Freezing, Oceans and Seas, Cold Temperature, Transcriptome, Mutation Rate, Evolution, Molecular, Recombination, Genetic, General Science & Technology
Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Published
2017

6. The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization

Author

Nishiyama, Tomoaki, Sakayama, Hidetoshi, de Vries, Jan, Buschmann, Henrik, Saint-Marcoux, Denis, Ullrich, Kristian K., Haas, Fabian B., Vanderstraeten, Lisa, Becker, Dirk, Lang, Daniel, Vosolsobě, Stanislav, Rombauts, Stephane, Wilhelmsson, Per K.I., Janitza, Philipp, Kern, Ramona, Heyl, Alexander, Rümpler, Florian, Villalobos, Luz Irina A. Calderón, Clay, John M., Skokan, Roman, Toyoda, Atsushi, Suzuki, Yutaka, Kagoshima, Hiroshi, Schijlen, Elio, Tajeshwar, Navindra, Catarino, Bruno, Hetherington, Alexander J., Saltykova, Assia, Bonnot, Clemence, Breuninger, Holger, Symeonidi, Aikaterini, Radhakrishnan, Guru V., Van Nieuwerburgh, Filip, Deforce, Dieter, Chang, Caren, Karol, Kenneth G., Hedrich, Rainer, Ulvskov, Peter, Glöckner, Gernot, Delwiche, Charles F., Petrášek, Jan, Van de Peer, Yves, Friml, Jiri, Beilby, Mary, Dolan, Liam, Kohara, Yuji, Sugano, Sumio, Fujiyama, Asao, Delaux, Pierre-Marc, Quint, Marcel, Theißen, Günter, Hagemann, Martin, Harholt, Jesper, Dunand, Christophe, Zachgo, Sabine, Langdale, Jane, Maumus, Florian, Van Der Straeten, Dominique, Gould, Sven B., and Rensing, Stefan A.

Published
2018
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8. The butterfly plant arms-race escalated by gene and genome duplications

Author

Edger, Patrick P., Heidel-Fischer, Hanna M., Bekaert, Michaël, Rota, Jadranka, Glöckner, Gernot, Platts, Adrian E., Heckel, David G., Der, Joshua P., Wafula, Eric K., Tang, Michelle, Hofberger, Johannes A., Smithson, Ann, Hall, Jocelyn C., Blanchette, Matthieu, Bureau, Thomas E., Wright, Stephen I., dePamphilis, Claude W., Schranz, M. Eric, Barker, Michael S., Conant, Gavin C., Wahlberg, Niklas, Vogel, Heiko, Pires, J. Chris, and Wheat, Christopher W.

Published
2015

9. The Genome of the Foraminiferan Reticulomyxa filosa

Author

Glöckner, Gernot, Hülsmann, Norbert, Schleicher, Michael, Noegel, Angelika A., Eichinger, Ludwig, Gallinger, Christoph, Pawlowski, Jan, Sierra, Roberto, Euteneuer, Ursula, Pillet, Loic, Moustafa, Ahmed, Platzer, Matthias, Groth, Marco, Szafranski, Karol, and Schliwa, Manfred

Published
2014
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11. Increased Heat Resilience of Intraspecific Outbred Compared to Inbred Lineages in the Kelp Laminaria digitata: Physiology and Transcriptomics

Author

Liesner, Daniel, Pearson, Gareth A., Bartsch, Inka, Rana, Shivani, Harms, Lars, Heinrich, Sandra, Bischof, Kai, Glöckner, Gernot, Valentin, Klaus-Ulrich, Liesner, Daniel, Pearson, Gareth A., Bartsch, Inka, Rana, Shivani, Harms, Lars, Heinrich, Sandra, Bischof, Kai, Glöckner, Gernot, and Valentin, Klaus-Ulrich

Abstract

Marine forests and kelps as their foundation species are threatened by ocean warming especially at the warm distributional edges. Previously identified genetic divergence and ecotypic differentiation within kelp species may allow to produce more resilient lineages by intraspecific outbreeding among populations. In a mechanistic investigation of heat stress, heterosis (hybrid vigour), and underlying gene expression patterns, we assessed the thermal performance of inbred (selfings) and outbred (reciprocal crosses) sporophytes of the N-Atlantic kelp Laminaria digitata among clonal isolates from two divergent populations; one from the temperate North Sea (Helgoland) and one from the Arctic (Spitsbergen). First, we investigated the upper thermal tolerance of microscopic sporophytes in a 14-day experiment applying sublethal to lethal 20–23°C. The upper survival temperature of microscopic sporophytes was lower for the inbred Arctic selfing (21°C) than for the temperate selfing and the reciprocal crosses (22°C). Only in the temperate selfing, 4.5% of sporophytes survived 23°C. We then subjected 4–7 cm long sporophytes to a control temperature (10°C), moderate (19°C) and sublethal to lethal heat stress (20.5°C) for 18 days to assess gene expression in addition to physiological parameters. Growth and optimum quantum yield decreased similarly in the reciprocal crosses and the temperate selfing at 19 and 20.5°C, while inbred Arctic sporophytes died within seven days at both 19 and 20.5°C. In response to 20.5°C, 252 genes were constitutively regulated across all surviving lineages, which we use to describe metabolic regulation patterns in response to heat stress in kelp. At sublethal 20.5°C, ca. 150 genes were differentially expressed by either crossed lineage in comparison to the temperate selfing, indicating that they maintained a growth response similar to the temperate selfing with differential metabolic regulation during sublethal heat stress. Subtle differences in physiolo

Published
2022

19. Transcriptomic Responses to Darkness and the Survival Strategy of the Kelp Saccharina latissima in the Early Polar Night

Author

Li, Huiru, Scheschonk, Lydia, Heinrich, Sandra, Valentin, Klaus, Harms, Lars, Glöckner, Gernot, Corre, Erwan, and Bischof, Kai

Abstract

Kelps in the Arctic region are facing challenging natural conditions. They experience over 120 days of darkness during the polar night surviving on storage compounds without conducting photosynthesis. Furthermore, the Arctic is experiencing continuous warming as a consequence of climate change. Such temperature increase may enhance the metabolic activity of kelps, using up storage compounds faster. As the survival strategy of kelps during darkness in the warming Arctic is poorly understood, we studied the physiological and transcriptomic responses of Saccharina latissima, one of the most common kelp species in the Arctic, after a 2-week dark exposure at two temperatures (0 and 4°C) versus the same temperatures under low light conditions. Growth rates were decreased in darkness but remained stable at two temperatures. Pigments had higher values in darkness and at 4°C. Darkness had a greater impact on the transcriptomic performance of S. latissima than increased temperature according to the high numbers of differentially expressed genes between dark and light treatments. Darkness generally repressed the expression of genes coding for glycolysis and metabolite biosynthesis, as well as some energy-demanding processes, such as synthesis of photosynthetic components and transporters. Moreover, increased temperature enhanced these repressions, while the expression of some genes encoding components of the lipid and laminaran catabolism, glyoxylate cycle and signaling were enhanced in darkness. Our study helps to understand the survival strategy of kelp in the early polar night and its potential resilience to the warming Arctic.

Published
2020

20. Increased heat resilience of intraspecific hybrids compared to inbred lineages of the kelp Laminaria digitata: physiology and transcriptomics

Author

Liesner, Daniel, Rana, Shivani, Harms, Lars, Pearson, Gareth A., Heinrich, Sandra, Bischof, Kai, Bartsch, Inka, Glöckner, Gernot, Valentin, Klaus-Ulrich, Liesner, Daniel, Rana, Shivani, Harms, Lars, Pearson, Gareth A., Heinrich, Sandra, Bischof, Kai, Bartsch, Inka, Glöckner, Gernot, and Valentin, Klaus-Ulrich

Abstract

Kelps, the marine forest foundation species, are threatened by ocean warming at their warm distributional edges. To mechanistically investigate inheritance of thermal traits, we assessed thermal tolerance of inbred (selfings) and outbred (crosses) sporophytes of the N-Atlantic kelp Laminaria digitata among isolates from the genetically distinct populations of Helgoland (North Sea) and Spitsbergen (Arctic). First, we investigated the upper thermal tolerance of microscopic sporophytes in a 14-day experiment applying 20–23°C. The upper survival temperature was lower for the Spitsbergen selfing (21°C) than for the Helgoland selfing and the reciprocal crosses (22°C). We then subjected 4–7 cm long sporophytes to a control temperature (10°C), moderate (19°C) and sub-lethal heat stress (20.5°C) to assess metabolic regulation via whole-transcriptome analysis in addition to physiological parameters. Growth and optimum quantum yield decreased similarly in both crosses and the Helgoland selfing at 19 and 20.5°C, while inbred Spitsbergen sporophytes died within seven days at both 19 and 20.5°C. At 10°C, the Spitsbergen selfing showed the highest differential gene expression. Considering only the three surviving lineages at 20.5°C, differential gene expression was 61–78% lower in the crosses compared to the Helgoland selfing, including reduced expression of transcripts related to cellular stress responses. This implies that both intraspecific crosses maintained a growth response similar to the Helgoland selfing with reduced metabolic regulation during sublethal heat stress, indicating subtle heterosis (hybrid vigour) as a beneficial effect of outbreeding. Results are discussed in the frame of mariculture and marine forest restoration.

Published
2021

24. Pan genome of the phytoplankton Emiliania underpins its global distribution

Author

Read, Betsy A., Kegel, Jessica, Klute, Mary J., Kuo, Alan, Lefebvre, Stephane C., Maumus, Florian, Mayer, Christoph, Miller, John, Monier, Adam, Salamov, Asaf, Young, Jeremy, Aguilar, Maria, Claverie, Jean-Michel, Frickenhaus, Stephan, Gonzalez, Karina, Herman, Emily K., Lin, Yao-Cheng, Napier, Johnathan, Ogata, Hiroyuki, Sarno, Analissa F., Shmutz, Jeremy, Schroeder, Declan, de Vargas, Colomban, Verret, Frederic, von Dassow, Peter, Valentin, Klaus, Van de Peer, Yves, Wheeler, Glen, Allen, Andrew E., Bidle, Kay, Borodovsky, Mark, Bowler, Chris, Brownlee, Colin, Cock, Mark J., Elias, Marek, Gladyshev, Vadim N., Groth, Marco, Guda, Chittibabu, Hadaegh, Ahmad, Debora Iglesias-Rodriguez, Maria, Jenkins, Jerry, Jones, Bethan M., Lawson, Tracy, Leese, Florian, Lindquist, Erika, Lobanov, Alexei, Lomsadze, Alexandre, Malik, Shehre-Banoo, Marsh, Mary E., Mackinder, Luke, Mock, Thomas, Mueller-Roeber, Bernd, Pagarete, António, Parker, Micaela, Probert, Ian, Quesneville, Hadi, Raines, Christine, Rensing, Stefan A., Riaño-Pachón, Diego Mauricio, Richier, Sophie, Rokitta, Sebastian, Shiraiwa, Yoshihiro, Soanes, Darren M., van der Giezen, Mark, Wahlund, Thomas M., Williams, Bryony, Wilson, Willie, Wolfe, Gordon, Wurch, Louie L., Dacks, Joel B., Delwiche, Charles F., Dyhrman, Sonya T., Glöckner, Gernot, John, Uwe, Richards, Thomas, Worden, Alexandra Z., Zhang, Xiaoyu, and Grigoriev, Igor V.

Published
2013
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25. Sequence and analysis of chromosome 2 of Dictyostelium discoideum

Author

Glöckner, Gernot, Eichinger, Ludwig, Szafranski, Karol, Pachebat, Justin A., Bankier, Alan T., Dear, Paul H., Lehmann, Rüdiger, Baumgart, Cornelia, Parra, Genís, Abril, Josep F., Guigó, Roderic, Kumpf, Kai, Tunggal, Budi, Cox, Edward, Quail, Michael A., Platzer, Matthias, Rosenthal, André, Noegel, Angelika A., Barrell, Bart G., Rajandream, Marie-Adèle, Williams, Jeffrey G., Kay, Robert R., Kuspa, Adam, Gibbs, Richard, Sucgang, Richard, Muzny, Donna, Desany, Brian, Zeng, Kathy, Zhu, Baoli, de Jong, Pieter, Dingermann, Theodor, Gerisch, Günther, Philippsen, Peter, Schleicher, Michael, Schuster, Stephan C., and Winckler, Thomas

Published
2002
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33. Temperature Modulates Sex-Biased Gene Expression in the Gametophytes of the Kelp Saccharina latissima

Author

Monteiro, Cátia, Heinrich, Sandra, Bartsch, Inka, Valentin, Klaus, Corre, Erwan, Collén, Jonas, Harms, Lars, Glöckner, Gernot, and Bischof, Kai

Abstract

Saccharina latissima is an economically and ecologically relevant kelp species in Europe and North America. In kelps, the sexuality is expressed during the haploid life stage and the microscopic gametophytes exhibit significant sexual dimorphism. To understand the sex-dependent impact of temperature on the gametophyte stage, we analyzed for the first time, gene expression profiles of male and female gametophytes at three different temperatures (4, 12, and 20°C) characteristic for the species distribution range by using RNA-sequencing. We identified several differentially expressed genes (DEGs) between sexes; while female biased genes were enriched in general metabolism and energy production, male biased genes function within cell cycle and signaling. In our study, temperature modulated sex-biased gene expression, with only a small percentage of DEGs consistently male (7%) or female-biased (12%) at the three temperatures. Female gametophytes responded stronger to higher temperatures than males, suggesting that males are more heat tolerant. Differences between S. latissima and other brown algal gender-dependent gene expression might mirror the different evolutionary and ecological contexts. Genomic information on kelp gametophyte is still scarce and thus this study adds to our knowledge on sex differences in abiotic stress responses in macroalgae at the transcriptomic level.

Published
2019

34. DNA sequence and analysis of human chromosome 8

Author

Nusbaum, Chad, Mikkelsen, Tarjei S., Zody, Michael C., Asakawa, Shuichi, Taudien, Stefan, Garber, Manuel, Kodira, Chinnappa D., Schueler, Mary G., Shimizu, Atsushi, Whittaker, Charles A., Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Yang, Xiaoping, Allen, Nicole R., Anderson, Scott, Asakawa, Teruyo, Blechschmidt, Karin, Bloom, Toby, Borowsky, Mark L., Butler, Jonathan, Cook, April, Corum, Benjamin, DeArellano, Kurt, DeCaprio, David, Dooley, Kathleen T., Dorris, Lester, III, Engels, Reinhard, Glöckner, Gernot, Hafez, Nabil, Hagopian, Daniel S., Hall, Jennifer L., Ishikawa, Sabine K., Jaffe, David B., Kamat, Asha, Kudoh, Jun, Lehmann, Rüdiger, Lokitsang, Tashi, Macdonald, Pendexter, Major, John E., Matthews, Charles D., Mauceli, Evan, Menzel, Uwe, Mihalev, Atanas H., Minoshima, Shinsei, Murayama, Yuji, Naylor, Jerome W., Nicol, Robert, Nguyen, Cindy, O'Leary, Sinéad B., O'Neill, Keith, Parker, Stephen C. J., Polley, Andreas, Raymond, Christina K., Reichwald, Kathrin, Rodriguez, Joseph, Sasaki, Takashi, Schilhabel, Markus, Siddiqui, Roman, Smith, Cherylyn L, Sneddon, Tam P., Talamas, Jessica A., Tenzin, Pema, Topham, Kerri, Venkataraman, Vijay, Wen, Gaiping, Yamazaki, Satoru, Young, Sarah K., Zeng, Qiandong, Zimmer, Andrew R., Rosenthal, Andre, Birren, Bruce W., Platzer, Matthias, Shimizu, Nobuyoshi, and Lander, Eric S.

Published
2006

35. Adaptive divergence across Southern Ocean gradients in the pelagic diatomFragilariopsis kerguelensis.

Author

Postel, U., Glemser, Barbara, Salazar Alekseyeva, Katherine, Eggers, S. L., Groth, Marco, Glöckner, Gernot, John, Uwe, Mock, Thomas, Klemm, Kerstin, Valentin, Klaus-Ulrich, Beszteri, Bank, Postel, U., Glemser, Barbara, Salazar Alekseyeva, Katherine, Eggers, S. L., Groth, Marco, Glöckner, Gernot, John, Uwe, Mock, Thomas, Klemm, Kerstin, Valentin, Klaus-Ulrich, and Beszteri, Bank

Abstract

The Southern Ocean is characterized by longitudinal water circulations crossed by strong latitudinal gradients. How this oceanographic background shapes planktonic populations is largely unknown, despite the significance of this region for global biogeochemical cycles. Here, we show, based on genomic, morphometric, ecophysiological and mating compatibility data, an example of ecotypic differentiation and speciation within an endemic pelagic inhabitant, the diatom Fragilariopsis kerguelensis. We discovered three genotypic variants, one present throughout the latitudinal transect sampled, the others restricted to the north and south, respectively. The latter two showed reciprocal monophyly across all three genomes and significant ecophysiological differences consistent with local adaptation, but produced viable offspring in laboratory crosses. The third group was also reproductively isolated from the latter two. We hypothesize that this pattern originated by an adaptive expansion accompanied by ecotypic divergence, followed by sympatric speciation.

Published
2020

37. The DNA sequence of the human X chromosome

Author

Ross, Mark T., Grafham, Darren V., Coffey, Alison J., Scherer, Steven, McLay, Kirsten, Muzny, Donna, Platzer, Matthias, Howell, Gareth R., Burrows, Christine, Bird, Christine P., Frankish, Adam, Lovell, Frances L., Howe, Kevin L., Ashurst, Jennifer L., Fulton, Robert S., Sudbrak, Ralf, Wen, Gaiping, Jones, Matthew C., Hurles, Matthew E., Andrews, T. Daniel, Scott, Carol E., Searle, Stephen, Ramser, Juliane, Whittaker, Adam, Deadman, Rebecca, Carter, Nigel P., Hunt, Sarah E., Chen, Rui, Cree, Andrew, Gunaratne, Preethi, Havlak, Paul, Hodgson, Anne, Metzker, Michael L., Richards, Stephen, Scott, Graham, Steffen, David, Sodergren, Erica, Wheeler, David A., Worley, Kim C., Ainscough, Rachael, Ambrose, Kerrie D., Ansari-Lari, M. Ali, Aradhya, Swaroop, Ashwell, Robert I. S., Babbage, Anne K., Bagguley, Claire L., Ballabio, Andrea, Banerjee, Ruby, Barker, Gary E., Barlow, Karen F., Barrett, Ian P., Bates, Karen N., Beare, David M., Beasley, Helen, Beasley, Oliver, Beck, Alfred, Bethel, Graeme, Blechschmidt, Karin, Brady, Nicola, Bray-Allen, Sarah, Bridgeman, Anne M., Brown, Andrew J., Brown, Mary J., Bonnin, David, Bruford, Elspeth A., Buhay, Christian, Burch, Paula, Burford, Deborah, Burgess, Joanne, Burrill, Wayne, Burton, John, Bye, Jackie M., Carder, Carol, Carrel, Laura, Chako, Joseph, Chapman, Joanne C., Chavez, Dean, Chen, Ellson, Chen, Guan, Chen, Yuan, Chen, Zhijian, Chinault, Craig, Ciccodicola, Alfredo, Clark, Sue Y., Clarke, Graham, Clee, Chris M., Clegg, Sheila, Clerc-Blankenburg, Kerstin, Clifford, Karen, Cobley, Vicky, Cole, Charlotte G., Conquer, Jen S., Corby, Nicole, Connor, Richard E., David, Robert, Davies, Joy, Davis, Clay, Davis, John, Delgado, Oliver, DeShazo, Denise, Dhami, Pawandeep, Ding, Yan, Dinh, Huyen, Dodsworth, Steve, Draper, Heather, Dugan-Rocha, Shannon, Dunham, Andrew, Dunn, Matthew, Durbin, K. James, Dutta, Ireena, Eades, Tamsin, Ellwood, Matthew, Emery-Cohen, Alexandra, Errington, Helen, Evans, Kathryn L., Faulkner, Louisa, Francis, Fiona, Frankland, John, Fraser, Audrey E., Galgoczy, Petra, Gilbert, James, Gill, Rachel, Glöckner, Gernot, Gregory, Simon G., Gribble, Susan, Griffiths, Coline, Grocock, Russell, Gu, Yanghong, Gwilliam, Rhian, Hamilton, Cerissa, Hart, Elizabeth A., Hawes, Alicia, Heath, Paul D., Heitmann, Katja, Hennig, Steffen, Hernandez, Judith, Hinzmann, Bernd, Ho, Sarah, Hoffs, Michael, Howden, Phillip J., Huckle, Elizabeth J., Hume, Jennifer, Hunt, Paul J., Hunt, Adrienne R., Isherwood, Judith, Jacob, Leni, Johnson, David, Jones, Sally, de Jong, Pieter J., Joseph, Shirin S., Keenan, Stephen, Kelly, Susan, Kershaw, Joanne K., Khan, Ziad, Kioschis, Petra, Klages, Sven, Knights, Andrew J., Kosiura, Anna, Kovar-Smith, Christie, Laird, Gavin K., Langford, Cordelia, Lawlor, Stephanie, Leversha, Margaret, Lewis, Lora, Liu, Wen, Lloyd, Christine, Lloyd, David M., Loulseged, Hermela, Loveland, Jane E., Lovell, Jamieson D., Lozado, Ryan, Lu, Jing, Lyne, Rachael, Ma, Jie, Maheshwari, Manjula, Matthews, Lucy H., McDowall, Jennifer, McLaren, Stuart, McMurray, Amanda, Meidl, Patrick, Meitinger, Thomas, Milne, Sarah, Miner, George, Mistry, Shailesh L., Morgan, Margaret, Morris, Sidney, Müller, Ines, Mullikin, James C., Nguyen, Ngoc, Nordsiek, Gabriele, Nyakatura, Gerald, O'Dell, Christopher N., Okwuonu, Geoffery, Palmer, Sophie, Pandian, Richard, Parker, David, Parrish, Julia, Pasternak, Shiran, Patel, Dina, Pearce, Alex V., Pearson, Danita M., Pelan, Sarah E., Perez, Lesette, Porter, Keith M., Ramsey, Yvonne, Reichwald, Kathrin, Rhodes, Susan, Ridler, Kerry A., Schlessinger, David, Schueler, Mary G., Sehra, Harminder K., Shaw-Smith, Charles, Shen, Hua, Sheridan, Elizabeth M., Shownkeen, Ratna, Skuce, Carl D., Smith, Michelle L., Sotheran, Elizabeth C., Steingruber, Helen E., Steward, Charles A., Storey, Roy, Swann, R. Mark, Swarbreck, David, Tabor, Paul E., Taudien, Stefan, Taylor, Tineace, Teague, Brian, Thomas, Karen, Thorpe, Andrea, Timms, Kirsten, Tracey, Alan, Trevanion, Steve, Tromans, Anthony C., d'Urso, Michele, Verduzco, Daniel, Villasana, Donna, Waldron, Lenee, Wall, Melanie, Wang, Qiaoyan, Warren, James, Warry, Georgina L., Wei, Xuehong, West, Anthony, Whitehead, Siobhan L., Whiteley, Mathew N., Wilkinson, Jane E., Willey, David L., Williams, Gabrielle, Williams, Leanne, Williamson, Angela, Williamson, Helen, Wilming, Laurens, Woodmansey, Rebecca L., Wray, Paul W., Yen, Jennifer, Zhang, Jingkun, Zhou, Jianling, Zoghbi, Huda, Zorilla, Sara, Buck, David, Reinhardt, Richard, Poustka, Annemarie, Rosenthal, André, Lehrach, Hans, Meindl, Alfons, Minx, Patrick J., Hillier, LaDeana W., Willard, Huntington F., Wilson, Richard K., Waterston, Robert H., Rice, Catherine M., Vaudin, Mark, Coulson, Alan, Nelson, David L., Weinstock, George, Sulston, John E., Durbin, Richard, Hubbard, Tim, Gibbs, Richard A., Beck, Stephan, Rogers, Jane, and Bentley, David R.

Published
2005

39. Lower Statistical Support with Larger Data Sets: Insights from the Ochrophyta Radiation.

Author

Franco, Arnaud Di, Baurain, Denis, Glöckner, Gernot, Melkonian, Michael, and Philippe, Hervé

Subjects
RADIATION, PHYLOGENETIC models, PHOTOSYNTHETIC reaction centers, PLASTIDS, MITOCHONDRIA
Abstract

It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid, and nucleus. Surprisingly while statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion (6,762 sites) and plastid (21,692 sites) trees, it decreases in the nuclear (209,105 sites) tree. Statistical support is not simply related to the data set size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that this ability for current phylogenetic methods is limited, because conflicting results were obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid data set provided higher statistical support for the ochrophyte radiation than the larger nucleus data set. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear data set. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of data sets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches. [ABSTRACT FROM AUTHOR]

Published
2022
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40. MOESM10 of Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima?

Author

Monteiro, Cátia Machado, Huiru Li, Bischof, Kai, Bartsch, Inka, Valentin, Klaus, Corre, Erwan, Collén, Jonas, Harms, Lars, Glöckner, Gernot, and Heinrich, Sandra

Abstract

Additional file 10. Phenotypic differences between sporophytes from Roscoff and Spitsbergen before the start of the experiment. A) Spitsbergen, B) Roscoff.

Published
2019
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43. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome

Author

John, Uwe, primary, Lu, Yameng, additional, Wohlrab, Sylke, additional, Groth, Marco, additional, Janouškovec, Jan, additional, Kohli, Gurjeet S., additional, Mark, Felix C., additional, Bickmeyer, Ulf, additional, Farhat, Sarah, additional, Felder, Marius, additional, Frickenhaus, Stephan, additional, Guillou, Laure, additional, Keeling, Patrick J., additional, Moustafa, Ahmed, additional, Porcel, Betina M., additional, Valentin, Klaus, additional, and Glöckner, Gernot, additional

Published
2019
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44. A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella

Author

Glöckner Gernot, Altincicek Boran, Vogel Heiko, and Vilcinskas Andreas

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The larvae of the greater wax moth Galleria mellonella are increasingly used (i) as mini-hosts to study pathogenesis and virulence factors of prominent bacterial and fungal human pathogens, (ii) as a whole-animal high throughput infection system for testing pathogen mutant libraries, and (iii) as a reliable host model to evaluate the efficacy of antibiotics against human pathogens. In order to compensate for the lack of genomic information in Galleria, we subjected the transcriptome of different developmental stages and immune-challenged larvae to next generation sequencing. Results We performed a Galleria transcriptome characterization on the Roche 454-FLX platform combined with traditional Sanger sequencing to obtain a comprehensive transcriptome. To maximize sequence diversity, we pooled RNA extracted from different developmental stages, larval tissues including hemocytes, and from immune-challenged larvae and normalized the cDNA pool. We generated a total of 789,105 pyrosequencing and 12,032 high-quality Sanger EST sequences which clustered into 18,690 contigs with an average length of 1,132 bases. Approximately 40% of the ESTs were significantly similar (E ≤ e-03) to proteins of other insects, of which 45% have a reported function. We identified a large number of genes encoding proteins with established functions in immunity related sensing of microbial signatures and signaling, as well as effector molecules such as antimicrobial peptides and inhibitors of microbial proteinases. In addition, we found genes known as mediators of melanization or contributing to stress responses. Using the transcriptomic data, we identified hemolymph peptides and proteins induced upon immune challenge by 2D-gelelectrophoresis combined with mass spectrometric analysis. Conclusion Here, we have developed extensive transcriptomic resources for Galleria. The data obtained is rich in gene transcripts related to immunity, expanding remarkably our knowledge about immune and stress-inducible genes in Galleria and providing the complete sequences of genes whose primary structure have only partially been characterized using proteomic methods. The generated data provide for the first time access to the genetic architecture of immunity in this model host, allowing us to elucidate the molecular mechanisms underlying pathogen and parasite response and detailed analyses of both its immune responses against human pathogens, and its coevolution with entomopathogens.

Published
2011
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45. Origin of land plants: Do conjugating green algae hold the key?

Author

Melkonian Michael, Philippe Hervé, Heidel Andrew J, Glöckner Gernot, Brinkmann Henner, Wodniok Sabina, and Becker Burkhard

Subjects
Evolution, QH359-425
Abstract

Abstract Background The terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial. Results Here, we use a large data set of nuclear-encoded genes (129 proteins) from 40 green plant taxa (Viridiplantae) including 21 embryophytes and six streptophyte algae, representing all major streptophyte algal lineages, to investigate the phylogenetic relationships of streptophyte algae and embryophytes. Our phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zygnematales and the Coleochaetales are the sister group to embryophytes. Conclusions Our analyses support the notion that the Charales are not the closest living relatives of embryophytes. Instead, the Zygnematales or a clade consisting of Zygnematales and Coleochaetales are most likely the sister group of embryophytes. Although this result is in agreement with a previously published phylogenetic study of chloroplast genomes, additional data are needed to confirm this conclusion. A Zygnematales/embryophyte sister group relationship has important implications for early land plant evolution. If substantiated, it should allow us to address important questions regarding the primary adaptations of viridiplants during the conquest of land. Clearly, the biology of the Zygnematales will receive renewed interest in the future.

Published
2011
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46. Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum

Author

Glöckner Gernot, Beszteri Sára, John Uwe, Yang Ines, Krock Bernd, Goesmann Alexander, and Cembella Allan D

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The dinoflagellate Alexandrium minutum typically produces paralytic shellfish poisoning (PSP) toxins, which are known only from cyanobacteria and dinoflagellates. While a PSP toxin gene cluster has recently been characterized in cyanobacteria, the genetic background of PSP toxin production in dinoflagellates remains elusive. Results We constructed and analysed an expressed sequence tag (EST) library of A. minutum, which contained 15,703 read sequences yielding a total of 4,320 unique expressed clusters. Of these clusters, 72% combined the forward-and reverse reads of at least one bacterial clone. This sequence resource was then used to construct an oligonucleotide microarray. We analysed the expression of all clusters in three different strains. While the cyanobacterial PSP toxin genes were not found among the A. minutum sequences, 192 genes were differentially expressed between toxic and non-toxic strains. Conclusions Based on this study and on the lack of identified PSP synthesis genes in the two existent Alexandrium tamarense EST libraries, we propose that the PSP toxin genes in dinoflagellates might be more different from their cyanobacterial counterparts than would be expected in the case of a recent gene transfer. As a starting point to identify possible PSP toxin-associated genes in dinoflagellates without relying on a priori sequence information, the sequences only present in mRNA pools of the toxic strain can be seen as putative candidates involved in toxin synthesis and regulation, or acclimation to intracellular PSP toxins.

Published
2010
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48. A first glimpse at the transcriptome of Physarum polycephalum

Author

Meyer Sonja, Werner-Felmayer Gabriele, Golderer Georg, Glöckner Gernot, and Marwan Wolfgang

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Physarum polycephalum, an acellular plasmodial species belongs to the amoebozoa, a major branch in eukaryote evolution. Its complex life cycle and rich cell biology is reflected in more than 2500 publications on various aspects of its biochemistry, developmental biology, cytoskeleton, and cell motility. It now can be genetically manipulated, opening up the possibility of targeted functional analysis in this organism. Methods Here we describe a large fraction of the transcribed genes by sequencing a cDNA library from the plasmodial stage of the developmental cycle. Results In addition to the genes for the basic metabolism we found an unexpected large number of genes involved in sophisticated signaling networks and identified potential receptors for environmental signals such as light. In accordance with the various developmental options of the plasmodial cell we found that many P. polycephalum genes are alternatively spliced. Using 30 donor and 30 acceptor sites we determined the splicing signatures of this species. Comparisons to various other organisms including Dictyostelium, the closest relative, revealed that roughly half of the transcribed genes have no detectable counterpart, thus potentially defining species specific adaptations. On the other hand, we found highly conserved proteins, which are maintained in the metazoan lineage, but absent in D. discoideum or plants. These genes arose possibly in the last common ancestor of Amoebozoa and Metazoa but were lost in D. discoideum. Conclusion This work provides an analysis of up to half of the protein coding genes of Physarum polycephalum. The definition of splice motifs together with the description of alternatively spliced genes will provide a valuable resource for the ongoing genome project.

Published
2008
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49. Responses of the kelp Saccharina latissima (Phaeophyceae) to the warming Arctic: from physiology to transcriptomics

Author

Li, Huiru, Monteiro, Catia, Heinrich, Sandra, Bartsch, Inka, Valentin, Klaus, Harms, Lars, Glöckner, Gernot, Corre, Erwan, Bischof, Kai, Li, Huiru, Monteiro, Catia, Heinrich, Sandra, Bartsch, Inka, Valentin, Klaus, Harms, Lars, Glöckner, Gernot, Corre, Erwan, and Bischof, Kai

Abstract

The Arctic region is currently facing substantial environmental changes due to global warming. Melting glaciers cause reduced salinity environments in coastal Arctic habitats, which may be stressful for kelp beds. To investigate the responses of the kelp Saccharina latissima to the warming Arctic, we studied the transcriptomic changes of S. latissima from Kongsfjorden (Svalbard, Norway) over a 24-hour exposure to two salinities (Absolute Salinity [SA] 20 and 30) after a 7-day pre-acclimation at three temperatures (0, 8 and 15∘C). In addition, corresponding physiological data were assessed during an 11-days salinity/temperature experiment. Growth and maximal quantum yield for photosystem II fluorescence were positively affected by increased temperature during acclimation, whereas hyposalinity caused negative effects at the last day of treatment. In contrast, hyposalinity induced marked changes on the transcriptomic level. Compared to the control (8∘C – SA 30), the 8∘C – SA 20 exhibited the highest number of differentially expressed genes (DEGs), followed by the 0∘C – SA 20. Comparisons indicate that S. latissima tends to convert its energy from primary metabolism (e.g. photosynthesis) to antioxidant activity under hyposaline stress. The increase in physiological performance at 15∘C shows that S. latissima in the Arctic region can adjust and might even benefit from increased temperatures. However, in Arctic fjord environments its performance might become impaired by decreased salinity as a result of ice melting.

Published
2019

50. Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima

Author

Monteiro, Catia, Li, Huiru, Bischof, Kai, Bartsch, Inka, Valentin, Klaus-Ulrich, Corre, Erwan, Collén, Jonas, Harms, Lars, Glöckner, Gernot, Heinrich, Sandra, Monteiro, Catia, Li, Huiru, Bischof, Kai, Bartsch, Inka, Valentin, Klaus-Ulrich, Corre, Erwan, Collén, Jonas, Harms, Lars, Glöckner, Gernot, and Heinrich, Sandra

Abstract

Background: Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far. Results: In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions – Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and SA 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (SA 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples. Conclusions: Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical c

Published
2019

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